Evidence map›Paper›PMID 39005434›Full record

ArticlebioRxiv : the preprint server for biology2024

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.

Tiffany A Kosch, María Torres-Sánchez, H Christoph Liedtke, Kyle Summers, Maximina H Yun, Andrew J Crawford, Simon T Maddock, Md Sabbir Ahammed, Victor L N Araújo, Lorenzo V Bertola and 38 more

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

48 authors.

Tiffany A KoschOne Health Research Group, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Werribee, Victoria, Australia.ORCID 0000-0001-5158-5748
María Torres-SánchezDepartment of Biodiversity, Ecology, and Evolution, Complutense University of Madrid, 28040 Madrid, Spain.ORCID 0000-0001-8484-9279
H Christoph LiedtkeEco-Evo-Devo Group, Estación Biológica de Doñana CSIC, Seville, Spain.ORCID 0000-0002-6221-8043
Kyle SummersBiology Department, East Carolina University, Greenville, NC, USA 27858.ORCID 0000-0001-7292-4286
Maximina H YunTechnische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, Dresden, Germany.ORCID 0000-0001-9019-2453
Andrew J CrawfordDepartment of Biological Sciences, Universidad de los Andes, Bogotá, 111711, Colombia.ORCID 0000-0003-3153-6898
Simon T MaddockSchool of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK.ORCID 0000-0002-5455-6990
Md Sabbir AhammedDepartment of Zoology, Jagannath University, Dhaka 1100, Bangladesh.ORCID 0009-0009-6967-0233
Victor L N AraújoDepartment of Biological Sciences, Universidad de los Andes, Bogotá, 111711, Colombia.
Lorenzo V BertolaCentre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4810, Australia.ORCID 0000-0002-1927-308X
Gary M BucciarelliDepartment of Wildlife, Fish, and Conservation Biology, University of California, Davis, USA.ORCID 0000-0003-3345-1361
Albert CarnéMuseo Nacional de Ciencias Naturales-CSIC, Madrid, Spain.ORCID 0000-0002-7920-8159
Céline M CarneiroDepartment of Integrative Biology, The University of Texas at Austin, Austin, TX, USA.ORCID 0000-0002-5266-4007
Kin O ChanUniversity of Kansas Biodiversity Institute and Natural History Museum, Lawrence, Kansas 66045, USA.ORCID 0000-0001-6270-0983
Ying ChenBiology Department, Queen's University, Kingston, Ontario, Canada.ORCID 0000-0002-2237-6426
Angelica CrottiniCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal.ORCID 0000-0002-8505-3050
Jessica M da SilvaEvolutionary Genomics and Wildlife Management, Foundatonal Biodiversity Science, Kirstenbosch Research Centre, South African National Biodiversity Institute, Newlands 7735, Cape Town, South Africa.ORCID 0000-0001-8385-1166
Robert D DentonDepartment of Biology, Marian University, Indianapolis, IN 46222, USA.ORCID 0000-0002-8629-1376
Carolin DittrichRojas Lab, Konrad-Lorenz-Institute of Ethology, Department of Life Science, University of Veterinary Medicine, Vienna, Austria.ORCID 0000-0002-4447-4481
Gonçalo Espregueira ThemudoCIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos, Portugal.ORCID 0000-0002-5019-9439
Katherine A FarquharsonSchool of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.ORCID 0000-0002-9009-7453
Natalie J ForsdickManaaki Whenua - Landcare Research, Auckland, New Zealand.ORCID 0000-0003-0423-3314
Edward GilbertSchool of Natural Sciences, The University of Hull, Hull, HU6 7RX, United Kingdom.ORCID 0000-0003-3273-1986
Jing CheKey Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.ORCID 0000-0003-4246-6514
Barbara A KatzenbackDepartment of Biology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1.ORCID 0000-0001-6171-5040
Ramachandran KotharambathHerpetology Lab, Dept. of Zoology, Central University of Kerala, Tejaswini Hills, Kasaragod, Kerala, 671320, India.
Nicholas A LevisDepartment of Biology, Indiana University, Bloomington, IN 47405, USA.ORCID 0000-0001-7650-2371
Roberto MárquezDepartment of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA.ORCID 0000-0002-0644-3078
Glib MazepaDepartment of Ecology and Evolution, University of Lausanne, Biophore, 1015, Switzerland.ORCID 0000-0001-6555-1434
Kevin P MulderWildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.ORCID 0000-0001-6688-8848
Hendrik MüllerCentral Natural Science Collections, Martin Luther University Halle-Wittenberg, D-06108 Halle (Saale), Germany.ORCID 0000-0001-6764-7376
Mary J O'ConnellSchool of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK.ORCID 0000-0002-1877-1001
Pablo Orozco-terWengelSchool of Biosciences, Cardiff University, Museum Avenue, CF10 3AX Cardiff, United Kingdom.ORCID 0000-0002-7951-4148
Gemma PalomarDepartment of Genetics, Physiology, and Microbiology; Faculty of Biological Sciences; Complutense University of Madrid, Madrid, Spain.ORCID 0000-0002-0659-8766
Alice PetzoldInstitute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Str.24-25, 14476 Potsdam, Germany.ORCID 0000-0002-0743-2004
David W PfennigDepartment of Biology, University of North Carolina, Chapel Hill, NC 27599, USA.ORCID 0000-0002-1114-534X
Karin S PfennigDepartment of Biology, University of North Carolina, Chapel Hill, NC 27599, USA.ORCID 0000-0002-0852-287X
Michael S ReichertDepartment of Integrative Biology, Oklahoma State University, Stillwater OK, USA.ORCID 0000-0002-0159-4387
Jacques RobertDepartment of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA.ORCID 0000-0003-4380-1476
Mark D ScherzNatural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen Ø, Denmark.ORCID 0000-0002-4613-7761
Karen Siu-TingSchool of Biological Sciences, Queen's University Belfast, Belfast, BT7 1NN, Northern Ireland, United Kingdom.ORCID 0000-0003-3698-1755
Anthony A SneadDepartment of Biology, New York University, New York, NY, USA.ORCID 0000-0002-5020-8729
Matthias StöckLeibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, D-12587 Berlin, Germany.ORCID 0000-0003-4888-8371
Adam M M StuckertDepartment of Biology and Biochemistry, University of Houston, Houston, Texas, 77204, USA.ORCID 0000-0003-2250-2223
Jennifer L StynoskiInstituto Clodomiro Picado, Universidad de Costa Rica, San José, Costa Rica.ORCID 0000-0002-9132-8567
Rebecca D TarvinMuseum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.ORCID 0000-0001-5387-7250
Katharina C Wollenberg ValeroSchool of Biology and Environmental Science, University College Dublin, Belfield Campus, Dublin 4, Ireland.ORCID 0000-0001-8858-1804
Amphibian Genomics Consortium (AGC)

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, antipredator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to "leap" to the next level.

Indexed as

AmphibiansBiodiversity conservationComparative genomicsGenomicsLissamphibiaMetagenomicsPhylogenomicsPopulation genomicsTaxonomyTranscriptomics

Identifiers

PMID39005434
PMCPMC11244923

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.